@article {70431,
	title = {De novo design of RNA pseudoknots with deep learning},
	journal = {bioRxiv},
	year = {2026},
	month = {2026 May 22},
	abstract = {<p>RNA design has been hindered by the limited accuracy of 3D structure prediction. Here, we show that intricate RNA structures can be generated with current deep learning tools through accurate de novo design of pseudoknot secondary structures. In an Eterna competition involving 57 pseudoknots, generative AI methods matched experienced human designers in solving most blind challenges, evaluated by single-nucleotide-resolution chemical mapping, compensatory mutagenesis, and cryogenic electron microscopy. Unexpectedly, AI-generated molecules with accurate secondary structures formed well-ordered 3D folds stabilized by noncanonical tertiary interactions not modeled during design. Success was guided by a RNet foundation model trained on prior chemical mapping data, suggesting that some difficult RNA design tasks may be tractable without first solving RNA 3D structure prediction.</p>
},
	doi = {10.64898/2026.05.21.726960},
	url = {https://www.biorxiv.org/content/early/2026/05/22/2026.05.21.726960},
	author = {Townley, Jill and Kladwang, Wipapat and Baker, David and Blair, Hamish M. and Choe, Christian A. and El Nesr, Gina and Favor, Andrew and Fisker, Eli and Haack, Daniel B. and He, Shujun and Hingey, Jason and Huang, Po-Ssu and Huang, Rui and Joshi, Chaitanya K. and Karagianes, Thomas and Kubaney, Andrew and Li{\`o}, Pietro and Mancino, Adamo and Romano, Jonathan and Rudolfs, Boris and Spellmon, Nicholas and Toor, Navtej and Wu, Vivian and Yu, Zhiheng and Eterna Participants and Das, Rhiju}
}
@article {70154,
	title = {LARGE1 processively polymerizes length-controlled matriglycan on prodystroglycan.},
	journal = {Nat Commun},
	volume = {16},
	year = {2025},
	month = {2025 Oct 10},
	pages = {9028},
	abstract = {<p>Matriglycan is a linear glycan (xylose-β1,3-glucuronate), which binds proteins in the extracellular matrix that contain laminin-globular domains and Lassa Fever Virus. It is indispensable for neuromuscular function. Matriglycan of insufficient length can cause muscular dystrophy with abnormal brain and eye development. LARGE1 (Like-acetylglucosaminyltransferase-1) uniquely synthesizes matriglycan on dystroglycan. The mechanism of matriglycan synthesis is not obvious from cryo-EM reconstructions of LARGE1. However, by reconstituting activity in vitro on recombinant prodystroglycan we show that the presence of the dystroglycan N-terminal domain (DGN), phosphorylated core M3, and a xylose-glucuronate primer are necessary for matriglycan polymerization by LARGE1. By introducing active site mutations, we demonstrate that LARGE1 processively polymerizes matriglycan on prodystroglycan, with its length regulated by the dystroglycan prodomain, DGN. Our enzymatic analysis of LARGE1 uncovers the mechanism of matriglycan synthesis on dystroglycan, which can form the basis for therapeutic strategies to treat matriglycan-deficient neuromuscular disorders and arenaviral infections.</p>
},
	keywords = {Animals, Catalytic Domain, Cryoelectron Microscopy, Dystroglycans, Humans, N-Acetylglucosaminyltransferases, Polymerization, Polysaccharides},
	issn = {2041-1723},
	doi = {10.1038/s41467-025-64080-z},
	url = {https://doi.org/10.1038/s41467-025-64080-z},
	author = {Joseph, Soumya and Schnicker, Nicholas J and Spellmon, Nicholas and Xu, Zhen and Yan, Rui and Yu, Zhiheng and Davulcu, Omar and Yang, Tiandi and Hopkins, Jesse and Anderson, Mary E and Venzke, David and Campbell, Kevin P}
}
